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Did Spybot mess up my computer? Please HELP

Windows XP
HP Pavilion a1310y
2.93 GHz
504 MB of RAM

Yesterday I downloaded Spybot Search & Destroy because I have a trojan giving me pop-up ads and now almost all the time Myspace, Google, Blogger, and popular email websites don't load. When I selected 'Fix selected problems' it gave me the error notification box with the X: 'Failed to load D:/Program Files/Spybot S&D\Delzip179.dll' and when I pressed OK: Unexpected error in fixing problems (out of memory). The boxes kept popping up, so I Ctrl alt Delete'd and scanned again. I think after it closed I got a bunch of prompts for me to approve the change of some important registry entries, and they had to do with the path name C:/Windows/system32, but I thought it was my system infected, so I might as well accept because Spybot was repairing only problems, not making mistakes... I became skeptical so I denied the rest. The next time I reset my computer I got these windows popping up with the black screen and the grey Courier text, having to do with C:/Windows/system32... About 50 of them popped up, and some had 'Could not find ____' (complex files of sorts).

I reset my computer to clearly write down what happens. Before shutting down, I get the warning box: Access violation at address 694c5405. Read of address 694c5405' with a blank OK button. I click it...
When the computer resets the black/grey windows say C:/Windows/system32/cmd.exe, C:/Windows/system32/command.com, C:/Windows/system32/ntvdm.exe on top, and ones that says 'Could not find apkgakxk.dll_old' and some with different dll-related names. These windows pop up then disappear quickly, by the way, but take a while until I can start using programs. Then the Spybot windows pop up after THAT... They say:

I am running the newest version. The access violation message wasn't from a program, but from my general computer - the box with the X that pops up accompanied by a sound. AND I don't know what AVG AV is...

It didn't say 'TeaTimer' on the 'registry change' messages, only Spybot S&D by itself... And it happened before I restarted, after the first successful scan and clicking 'fix problems.' Spybot caused those black windows to come up, depending on either the small amount of times I clicked 'accept' or all of the clicking 'deny'... I want to know if Spybot possibly ever effects important dll's in the Windows/system32 folder and causes drastic problems like slow startup, those black windows popping up forever, etc... because I learned to never alter things in the Windows folder and Dll's - they're vital. So I'm confused as to whether or not saying 'accept change' causes damage or Spybot is repairing a change made by the spyware/virus/trojan.

Also, yes I can still see my desktop fine. Although for some reason after this, my quick launch icons disappeared - the buttons at the bottom right of my Start bar.

That startup entry was created by the Spybot "Fix selected problems" facility to attempt to delete a problem during your system startup. By not allowing the deletion of that particular entry it will continue to execute each time you restart your system.

Getting an answer is one thing, learning is another.

Microsoft Windows XP Home Edition running on a 2.40GHz IntelŪ PentiumŪ 4 Processor with 512 MB of RAM and a 533 MHz System Bus.

To add to md's post about accepting the change, also to change whether "Quick Launch" shows up, right-click on the taskbar and click on "Properties". You should be able to see what displays on your taskbar (place where START is).

oh noes

I've had the exactly same problems, and the exactly same code when I restart. 694C5405. This happened to me to right after I got the evil trojan. The trojans name was Virtumonde. It said I was required to restart on the Description, and thats exactly what I did, and I get those evil numbers 694C5405. Then it started up a 20 minute search O_O. When it was back up theres like 20 registry changes by Spybot, I accepted them all. Im not sure if I still have the trojan, but I'm pretty definite that it makes wronchy stuff pop up occasionaly. I will restart my computer 1 more time and when I get back and theres still a error I will tell you guys if the trojan isnt comming off my computer.